@phdthesis{Boehm2023,
  author    = {B{\"o}hm, Christoph},
  title     = {Thermal Stability of the Polyesters PCL and PLGA during Melt Electrowriting},
  doi       = {10.25972/OPUS-30613},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-306139},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {The focus of this thesis was to investigate how PCL and PLGA react to the heat exposure that comes with the MEW process over a defined timespan. To assess the thermal stability of PCL during MEW over 25 d, an automated collection of fibers has been used to determine the CTS on each day of heating for three different temperatures. PCL is exceptionally stable over 25 d at 75 °C, whereas for 85 °C and 95 °C a slight upward trend during the last 10 d could be observed, which is an indication for thermal degradation. Same trend could be observed for diameter of fibers produced at a fixed collector speed. For all temperatures, CTS during the first 5 d decreased due to inhomogeneities of the melt. Physical analysis of the fibers by XRD and mechanical testing showed no significant changes. To investigate the chemical details of the thermal durability, PCL was artificially aged over 25 d at 75 °C, 85 °C and 95 °C. Data from GPC analysis and rheology revealed that PCL is degrading steadily at all three temperatures. Combined with GC-MS analysis, two different mechanisms for degradation could be observed: random chain scission and unzipping. Additional GPC experiment using a mixture of PCL and a fluorescence labelled PCL showed that PCL was undergoing ester interchange reactions, which could explain its thermal stability. PLGA was established successfully as material for MEW. GPC results revealed that PLGA degraded heavily in the one-hour preheating period. To reduce the processing temperature, ATEC was blended with PLGA in three mixtures. This slowed down degradation and a processing window of 6 h could be established. Mechanical testing with fibers produced with PLGA and all three blends was performed. PLGA was very brittle, whereas the blends showed an elastic behavior. This could be explained by ester interchange reactions that formed a loosely crosslinked network with ATEC.},
  subject      = {Degradation},
  language  = {en}
}
@phdthesis{Gold2023,
  author    = {Gold, Lukas},
  title     = {Methods for the state estimation of lithium-ion batteries},
  doi       = {10.25972/OPUS-30618},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-306180},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {This work introduced the reader to all relevant fields to tap into an ultrasound-based state of charge estimation and provides a blueprint for the procedure to achieve and test the fundamentals of such an approach. It spanned from an in-depth electrochemical characterization of the studied battery cells over establishing the measurement technique, digital processing of ultrasonic transmission signals, and characterization of the SoC dependent property changes of those signals to a proof of concept of an ultrasound-based state of charge estimation. The State of the art \& theoretical background chapter focused on the battery section on the mechanical property changes of lithium-ion batteries during operation. The components and the processes involved to manufacture a battery cell were described to establish the fundamentals for later interrogation. A comprehensive summary of methods for state estimation was given and an emphasis was laid on mechanical methods, including a critical review of the most recent research on ultrasound-based state estimation. Afterward, the fundamentals of ultrasonic non-destructive evaluation were introduced, starting with the sound propagation modes in isotropic boundary-free media, followed by the introduction of boundaries and non-isotropic structure to finally approach the class of fluid-saturated porous media, which batteries can be counted to. As the processing of the ultrasonic signals transmitted through lithium-ion battery cells with the aim of feature extraction was one of the main goals of this work, the fundamentals of digital signal processing and methods for the time of flight estimation were reviewed and compared in a separate section. All available information on the interrogated battery cell and the instrumentation was collected in the Experimental methods \& instrumentation chapter, including a detailed step-by-step manual of the process developed in this work to create and attach a sensor stack for ultrasonic interrogation based on low-cost off-the-shelf piezo elements. The Results \& discussion chapter opened with an in-depth electrochemical and post-mortem interrogation to reverse engineer the battery cell design and its internal structure. The combination of inductively coupled plasma-optical emission spectrometry and incremental capacity analysis applied to three-electrode lab cells, constructed from the studied battery cell's materials, allowed to identify the SoC ranges in which phase transitions and staging occur and thereby directly links changes in the ultrasonic signal properties with the state of the active materials, which makes this work stand out among other studies on ultrasound-based state estimation. Additional dilatometer experiments were able to prove that the measured effect in ultrasonic time of flight cannot originate from the thickness increase of the battery cells alone, as this thickness increase is smaller and in opposite direction to the change in time of flight. Therefore, changes in elastic modulus and density have to be responsible for the observed effect. The construction of the sensor stack from off-the-shelf piezo elements, its electromagnetic shielding, and attachment to both sides of the battery cells was treated in a subsequent section. Experiments verified the necessity of shielding and its negligible influence on the ultrasonic signals. A hypothesis describing the metal layer in the pouch foil to be the transport medium of an electrical coupling/distortion between sending and receiving sensor was formulated and tested. Impedance spectroscopy was shown to be a useful tool to characterize the resonant behavior of piezo elements and ensure the mechanical coupling of such to the surface of the battery cells. The excitation of the piezo elements by a raised cosine (RCn) waveform with varied center frequency in the range of 50 kHz to 250 kHz was studied in the frequency domain and the influence of the resonant behavior, as identified prior by impedance spectroscopy, on waveform and frequency content was evaluated to be uncritical. Therefore, the forced oscillation produced by this excitation was assumed to be mechanically coupled as ultrasonic waves into the battery cells. The ultrasonic waves transmitted through the battery cell were recorded by piezo elements on the opposing side. A first inspection of the raw, unprocessed signals identified the transmission of two main wave packages and allowed the identification of two major trends: the time of flight of ultrasonic wave packages decreases with the center frequency of the RCn waveform, and with state of charge. These trends were to be assessed further in the subsequent sections. Therefore, methods for the extraction of features (properties) from the ultrasonic signals were established, compared, and tested in a dedicated section. Several simple and advanced thresholding methods were compared with envelope-based and cross-correlation methods to estimate the time of flight (ToF). It was demonstrated that the envelope-based method yields the most robust estimate for the first and second wave package. This finding is in accordance with the literature stating that an envelope-based method is best suited for dispersive, absorptive media [204], to which lithium-ion batteries are counted. Respective trends were already suggested by the heatmap plots of the raw signals vs. RCn frequency and SoC. To enable such a robust estimate, an FIR filter had to be designed to preprocess the transmitted signals and thereby attenuate frequency components that verifiably lead to a distorted shape of the envelope. With a robust ToF estimation method selected, the characterization of the signal properties ToF and transmitted energy content (EC) was performed in-depth. A study of cycle-to-cycle variations unveiled that the signal properties are affected by a long rest period and the associated relaxation of the multi-particle system "battery cell" to equilibrium. In detail, during cycling, the signal properties don't reach the same value at a given SoC in two subsequent cycles if the first of the two cycles follows a long rest period. In accordance with the literature, a break-in period, making up for more than ten cycles post-formation, was observed. During this break-in period, the mechanical properties of the system are said to change until a steady state is reached [25]. Experiments at different C-rate showed that ultrasonic signal properties can sense the non-equilibrium state of a battery cell, characterized by an increasing area between charge and discharge curve of the respective signal property vs. SoC plot. This non-equilibrium state relaxes in the rest period following the discharge after the cut-off voltage is reached. The relaxation in the rest period following the charge is much smaller and shows little C-rate dependency as the state is prepared by constant voltage charging at the end of charge voltage. For a purely statistical SoC estimation approach, as employed in this work, where only instantaneous measurements are taken into account and the historic course of the measurement is not utilized as a source of information, the presence of hysteresis and relaxation leads to a reduced estimation accuracy. Future research should address this issue or even utilize the relaxation to improve the estimation accuracy, by incorporating historic information, e.g., by using the derivative of a signal property as an additional feature. The signal properties were then tested for their correlation with SoC as a function of RCn frequency. This allowed identifying trends in the behavior of the signal properties as a function of RCn frequency and C-rate in a condensed fashion and thereby enabled to predict the frequency range, about 50 kHz to 125 kHz, in which the course of the signal properties is best suited for SoC estimation. The final section provided a proof of concept of the ultrasound-based SoC estimation, by applying a support vector regression (SVR) to before thoroughly studied ultrasonic signal properties, as well as current and battery cell voltage. The included case study was split into different parts that assessed the ability of an SVR to estimate the SoC in a variety of scenarios. Seven battery cells, prepared with sensor stacks attached to both faces, were used to generate 14 datasets. First, a comparison of self-tests, where a portion of a dataset is used for training and another for testing, and cross-tests, which use the dataset of one cell for training and the dataset of another for testing, was performed. A root mean square error (RMSE) of 3.9\% to 4.8\% SoC and 3.6\% to 10.0\% SoC was achieved, respectively. In general, it was observed that the SVR is prone to overestimation at low SoCs and underestimation at high SoCs, which was attributed to the pronounced hysteresis and relaxation of the ultrasonic signal properties in this SoC ranges. The fact that higher accuracy is achieved, if the exact cell is known to the model, indicates that a variation between cells exists. This variation between cells can originate from differences in mechanical properties as a result of production variations or from differences in manual sensor placement, mechanical coupling, or resonant behavior of the ultrasonic sensors. To mitigate the effect of the cell-to-cell variations, a test was performed, where the datasets of six out of the seven cells were combined as training data, and the dataset of the seventh cell was used for testing. This reduced the spread of the RMSE from (3.6 - 10.0)\% SoC to (5.9 - 8.5)\% SoC, respectively, once again stating that a databased approach for state estimation becomes more reliable with a large data basis. Utilizing self-tests on seven datasets, the effect of additional features on the state estimation result was tested. The involvement of an additional feature did not necessarily improve the estimation accuracy, but it was shown that a combination of ultrasonic and electrical features is superior to the training with these features alone. To test the ability of the model to estimate the SoC in unknown cycling conditions, a test was performed where the C-rate of the test dataset was not included in the training data. The result suggests that for practical applications it might be sufficient to perform training with the boundary of the use cases in a controlled laboratory environment to handle the estimation in a broad spectrum of use cases. In comparison with literature, this study stands out by utilizing and modifying off-the-shelf piezo elements to equip state-of-the-art lithium-ion battery cells with ultrasonic sensors, employing a range of center frequencies for the waveform, transmitted through the battery cell, instead of a fixed frequency and by allowing the SVR to choose the frequency that yields the best result. The characterization of the ultrasonic signal properties as a function of RCn frequency and SoC and the assignment of characteristic changes in the signal properties to electrochemical processes, such as phase transitions and staging, makes this work unique. By studying a range of use cases, it was demonstrated that an improved SoC estimation accuracy can be achieved with the aid of ultrasonic measurements - thanks to the correlation of the mechanical properties of the battery cells with the SoC.},
  subject      = {Lithium-Ionen-Akkumulator},
  language  = {en}
}
@phdthesis{Bothe2021,
  author    = {Bothe, Sebastian Helmut},
  title     = {Fragmentbasiertes Design von p97-Liganden: Identifizierung von Startstrukturen zur Entwicklung von Protein-Protein-Interaktionsinhibitoren f{\"u}r die SHP-Bindestelle der AAA+ ATPase p97},
  doi       = {10.25972/OPUS-23911},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-239112},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {Die AAA+ ATPase p97 ist ein essenzielles Protein, das an einer Vielzahl zellul{\"a}rer Prozesse beteiligt ist und eine Schl{\"u}sselrolle in der Protein-Hom{\"o}ostase spielt. Die funktionale Diversit{\"a}t von p97 beruht auf der Interaktion zahlreicher unterschiedlicher Kofaktoren, die vorwiegend an die N-Dom{\"a}ne von p97 binden. Aufgrund seiner Bedeutung in der Regulierung diverser physiologischer und pathologischer Prozesse stellt p97 eine interessante Zielstruktur f{\"u}r die Entwicklung neuer Wirkstoffe dar, die insbesondere in der Krebstherapie von Bedeutung sein k{\"o}nnte. Bekannte p97-Inhibitoren greifen vor allem die ATPase-Funktion des Proteins an. Ein neuer pharmakologischer Ansatz stellt die Inhibierung der Kofaktorbindung an die N-Dom{\"a}ne dar. Ein solcher Protein-Protein-Interaktionsinhibitor w{\"a}re nicht nur von therapeutischem Interesse, sondern h{\"a}tte auch einen besonderen Nutzen f{\"u}r die Entschl{\"u}sselung molekularer und zellul{\"a}rer Funktionen von p97-Kofaktoren. In dieser Arbeit wurde ein fragmentbasierter Ansatz f{\"u}r die Identifizierung von chemischen Startstrukturen f{\"u}r die Entwicklung eines Protein-Protein- Interaktionsinhibitors verfolgt. Als Zielstruktur wurde die SHP-Bindestelle in der N-Dom{\"a}ne gew{\"a}hlt. Die Identifizierung von Liganden erfolgte sowohl durch computergest{\"u}tzte Methoden (insbesondere virtuelles Screening und Molekulardynamik-Simulationen) als auch experimentell durch biophysikalische Techniken (wie Biolayer-Interferometrie, R{\"o}ntgenstrukturanalyse und ligandbasierte NMR-Techniken). Die Grundlage des computerbasierten Designs stellte eine Analyse der bekannten Kristallstrukturen der p97-Komplexe mit den SHP-Motiven der Kofaktoren UFD1 und Derlin-1 dar. Dar{\"u}ber hinaus dienten Molekulardynamik-Simulationen der Analyse der Wassereigenschaften innerhalb der SHP-Bindestelle. Darauf aufbauend wurden verschiedene Pharmakophormodelle entwickelt, die die Grundlage des im Anschluss durchgef{\"u}hrten virtuellen Screenings und Dockings bildeten. Anhand der Ergebnisse von Molekulardynamik-Simulationen wurden zehn Verbindungen f{\"u}r die experimentelle Validierung ausgew{\"a}hlt. Hiervon konnten zwei Fragmente in STD-NMR- und Biolayer-Interferometrie-Experimenten als Liganden best{\"a}tigt werden. In einem parallel durchgef{\"u}hrten biophysikalischen Fragmentscreening mittels Biolayer-Interferometrie wurden unter mehr als 650 Verbindungen 22 identifiziert, die an die N-Dom{\"a}ne binden. 15 dieser Fragmente wurden durch einen orthogonalen STD-NMR-Assay best{\"a}tigt. F{\"u}nf dieser Verbindungen zeigten Affinit{\"a}ten mit KD-Werten kleiner 500μMund g{\"u}nstigen Ligandeffizienzen. Des Weiteren konnte die Bindungskinetik und Affinit{\"a}t des in der Literatur als p97-Inhibitor berichteten Naturstoffes Xanthohumol bestimmt und eine Bindung an die N-Dom{\"a}ne best{\"a}tigt werden. Zur Identifizierung m{\"o}glicher Bindestellen dieser f{\"u}nf Fragmente wurden mixed-solvent Molekulardynamik-Simulationen durchgef{\"u}hrt. Diese ergaben, dass alle Verbindungen die SHP-Bindestelle in der N-Dom{\"a}ne adressieren. Die Regionen fielen mit hot spots der Kofaktorwechselwirkungen zusammen und stellen somit m{\"o}gliche Ankerpunkte f{\"u}r die Weiterentwicklung dar. F{\"u}r zwei Fragmente konnten die postulierten Bindestellen mittels R{\"o}ntgenstrukturanalyse bzw. STD-NMR-Messungen an p97-Alanin-Mutanten best{\"a}tigt werden. Die erhaltene R{\"o}ntgenstruktur ist die erste p97-Struktur, die ein gebundenes Fragment an der N-Dom{\"a}ne zeigt.},
  subject      = {Arzneimitteldesign},
  language  = {de}
}
@article{StaabLotterMuehleetal.2021,
  author    = {Staab, Torsten E. M. and Lotter, Frank and M{\"u}hle, Uwe and Elsayed, Mohamed and Petschke, Danny and Schubert, Thomas and Ibrahim, Alaa M. and Krause-Rehberg, Reinhard and Kieback, Bernd},
  title     = {The decomposition process in high-purity Al-1.7 at.\% Cu alloys with trace elements: preservation of quenched-in vacancies by In, Sn and Pb influencing the ​θ′formation},
  series = {Journal of Materials Science},
  volume    = {56},
  journal   = {Journal of Materials Science},
  number    = {14},
  issn      = {1573-4803},
  doi       = {10.1007/s10853-020-05742-9},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-269103},
  pages     = {8717-8731},
  year      = {2021},
  abstract  = {Aluminium-copper alloys of the 2xxx type receive their excellent mechanical properties by the formation of copper-rich precipitates during hardening. Size, distribution and crystal structure of the formed precipitates determine the final strength of those alloys. Adding traces of certain elements, which bind to vacancies, significantly influences the decomposition behaviour, i.e. the diffusion of the copper atoms. For high-purity ternary alloys (Al-1.7 at.\% Cu-X), we investigate the interaction of copper and trace element atoms (X=In, Sn, and Pb) with quenched-in vacancies by Positron Annihilation Lifetime Spectroscopy (PALS). By employing Vickers microhardness, Differential Scanning Calorimetry (DSC) and Small Angle X-Ray Scattering (SAXS) we obtain a comprehensive picture of the decomposition process: opposite to predicted binding energies to vacancies by ab-initio calculations we find during ageing at room and elevated temperature a more retarded clustering of copper in the presence of In rather than for Sn additions, while Pb, having the highest predicted binding to vacancies, shows nearly no retarding effect compared to pure Al-Cu. If the latter would be due to a limited solubility of lead, it had to be below 2 ppm. Transmission Electron Microscopy (TEM) as imaging method complements our findings. Annealing the quenched Al-1.7 at.\% Cu-X-alloys containing 100 ppm In or Sn at 150∘C leads to finely distributed θ′-precipitates on the nanoscale, since due to the trace additions the formation temperature of θ′ is lowered by more than 100∘C. According to TEM small agglomerates of trace elements (In, Sn) may support the early nucleation for the θ′-precipitates.},
  language  = {en}
}
@phdthesis{He2024,
  author    = {He, Feng},
  title     = {Drug Discovery based on Oxidative Stress and HDAC6 for Treatment of Neurodegenerative Diseases},
  doi       = {10.25972/OPUS-25349},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-253497},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2024},
  abstract  = {Most antioxidants reported so far only achieved limited success in AD clinical trials. Growing evidences suggest that merely targeting oxidative stress will not be sufficient to fight AD. While multi-target directed ligands could synergistically modulate different steps in the neurodegenerative process, offering a promising potential for treatment of this complex disease. Fifteen target compounds have been designed by merging melatonin and ferulic acid into the cap group of a tertiary amide HDAC6 inhibitor. Compound 10b was screened as the best hybrid molecule exhibit potent HDAC6 inhibition and potent antioxidant capacity. Compound 10b also alleviated LPS-induced microglia inflammation and led to a switch from neurotoxic M1 to the neuroprotective M2 microglial phenotype. Moreover, compound 10b show pronounced attenuation of spatial working memory and long-term memory damage in an in vivo AD mouse model. Compound 10b can be a potentially effective drug candidate for treatment of AD and its druggability worth to be further studied. We have designed ten novel neuroprotectants by hybridizing with several common antioxidants, including ferulic acid, melatonin, lipoic acid, and trolox. The trolox hybrid compound exhibited the most potent neuroprotective effects in multiple neuroprotection assays. Besides, we identified the synergistic effects between trolox and vitamin K derivative, and our trolox hybrid compound showed comparable neuroprotection with the mixture of trolox and vitamin K derivative. We have designed and synthesized 24 quinone derivatives based on five kinds of different quinones including ubiquinone, 2,3,5-trimethyl-1,4-benzoquinone, memoquin, thymoquinone, and anthraquinone. Trimethylbenzoquinone and thymoquinone derivatives showed more potent neuroprotection than other quinones in oxytosis assay. Therefore, trimethylbenzoquinone and thymoquinone derivatives can be used as lead compounds for further mechanism study and drug discovery for treatment of neurodegenerative disease. We designed a series of photoswitchable HDAC inhibitors, which could be effective molecular tools due to the high spatial and temporal resolution. In total 23 target compounds were synthesized and photophysicochemically characterized. Azoquinoline-based compounds possess more thermally stable cis-isomers in buffer solution, which were further tested in enzyme-based HDAC inhibition assay. However, none of those tested compounds show significant differences in activities between trans-isomers and corresponding cis-isomers.},
  subject      = {Alzheimerkrankheit},
  language  = {en}
}
@phdthesis{Bozkaya2023,
  author    = {Bozkaya, Beg{\"u}m},
  title     = {Influence of Carbon Additives on the Electrochemical Performance of Modern Lead-Acid Batteries},
  doi       = {10.25972/OPUS-31917},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-319174},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {In the first part of this thesis, a validation of both short-term and long-term DCA tests on 2 V laboratory cells is focussed. The aim is to improve the laboratory cell level measurement technology for dynamic charge acceptance regarding the investigation of carbon additives. To address this issue, it is crucial to apply carbon additives generating a remarkable difference in charge acceptance. For this purpose, five different carbon additives providing a variation in the specific external surface were included as additives in the negative plates of 2 V lead-acid cells. Both short-term (charge acceptance test 2 from SBA and DCA from EN) and long-term (Run-in DCA from Ford) DCA tests were executed on the lead-acid cells. Further understanding of the mechanism was studied by applying electrochemical methods like cyclic voltammetry and electrochemical impedance spectroscopy. The second part of this thesis aims to understand the impact of carbon surface functional groups on the electrochemical activity of the negative electrodes as well as the DCA of 2 V lead-acid cells. In order to address this topic, commercially available activated carbon was modified by different chemical treatments to incorporate specific surface functional groups in the carbon structure. A series of activated carbons having a broad range of pH was prepared, which were used as additives in the negative electrodes. The corresponding lead-acid cells were subjected to cyclic voltammetry and DCA test according to EN. Further, the physical and chemical properties of the functionalized carbon additives were intensively analyzed to establish a structure-property relationship with a focus on DCA.},
  subject      = {Bleiakkumulator},
  language  = {en}
}
@phdthesis{Halmen2021,
  author    = {Halmen, Norbert},
  title     = {Vernetzungsgrad unter der Lupe : Zerst{\"o}rungsfreie Pr{\"u}fung mit unilateraler NMR},
  publisher = {W{\"u}rzburg University Press},
  address   = {W{\"u}rzburg},
  isbn      = {978-3-95826-160-0},
  doi       = {10.25972/WUP-978-3-95826-161-7},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-233506},
  school      = {W{\"u}rzburg University Press},
  pages     = {xv, 182},
  year      = {2021},
  abstract  = {Der Vernetzungsgrad von Klebstoffen und strahlenvernetzter Kunststoffformteile beeinflusst zahlreiche Materialeigenschaften und ist von essenzieller Bedeutung f{\"u}r die Funktionalit{\"a}t von Klebeverbindungen und die Best{\"a}ndigkeit medizinischer Implantate. Die zerst{\"o}rungsfreie Pr{\"u}fung dieser Qualit{\"a}tsgr{\"o}ße ist von großem industriellem Interesse, aber noch nicht Stand der Technik. Die unilaterale Kernspinresonanz (uNMR) ist ein vielversprechendes Verfahren zur L{\"o}sung dieser Problematik. In diesem Buch wird die nicht-invasive Vernetzungsgradpr{\"u}fung von strahlenvernetztem UHMWPE und verschiedenen Klebstoffen mittels uNMR demonstriert. Auf Basis der guten Korrelation mit praxisrelevanten Referenzmethoden (thermisch, rheologisch, dielektrisch) wurden Vergleichsmodelle entwickelt, welche Anwendern von Klebstoffen und vernetzten Kunststoffformteilen den Einsatz der uNMR zur zerst{\"o}rungsfreien Qualit{\"a}tssicherung erm{\"o}glichen.},
  subject      = {Magnetische Kernresonanz},
  language  = {de}
}
@article{CzyschMedina‐MontanoZhongetal.2022,
  author    = {Czysch, Christian and Medina-Montano, Carolina and Zhong, Zifu and Fuchs, Alexander and Stickdorn, Judith and Winterwerber, Pia and Schmitt, Sascha and Deswarte, Kim and Raabe, Marco and Scherger, Maximilian and Combes, Francis and De Vrieze, Jana and Kasmi, Sabah and Sandners, Niek N. and Lienenklaus, Stefan and Koynov, Kaloian and R{\"a}der, Hans-Joachim and Lambrecht, Bart N. and David, Sunil A. and Bros, Matthias and Schild, Hansj{\"o}rg and Grabbe, Stephan and De Geest, Bruno G. and Nuhn, Lutz},
  title     = {Transient Lymph Node Immune Activation by Hydrolysable Polycarbonate Nanogels},
  series = {Advanced Functional Materials},
  volume    = {32},
  journal   = {Advanced Functional Materials},
  number    = {35},
  doi       = {10.1002/adfm.202203490},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-287255},
  year      = {2022},
  abstract  = {The development of controlled biodegradable materials is of fundamental importance in immunodrug delivery to spatiotemporally controlled immune stimulation but avoid systemic inflammatory side effects. Based on this, polycarbonate nanogels are developed as degradable micellar carriers for transient immunoactivation of lymph nodes. An imidazoquinoline-type TLR7/8 agonist is covalently conjugated via reactive ester chemistry to these nanocarriers. The nanogels not only provide access to complete disintegration by the hydrolysable polymer backbone, but also demonstrate a gradual disintegration within several days at physiological conditions (PBS, pH 6.4-7.4, 37 °C). These intrinsic properties limit the lifetime of the carriers but their payload can still be successfully leveraged for immunological studies in vitro on primary immune cells as well as in vivo. For the latter, a spatiotemporal control of immune cell activation in the draining lymph node is found after subcutaneous injection. Overall, these features render polycarbonate nanogels a promising delivery system for transient activation of the immune system in lymph nodes and may consequently become very attractive for further development toward vaccination or cancer immunotherapy. Due to the intrinsic biodegradability combined with the high chemical control during the manufacturing process, these polycarbonate-based nanogels may also be of great importance for clinical translation.},
  language  = {en}
}
@phdthesis{Pinzner2021,
  author    = {Pinzner, Florian},
  title     = {Vicinal and Double Chemoselective Biofunctionalization of Polyoxazolines},
  doi       = {10.25972/OPUS-22975},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-229758},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {In this work, a toolbox was provided to create three-component polymer conjugates with a defined architecture, designed to bear different biocomponents that can interact with larger biological systems in biomacromolecular recognition experiments. The target architecture is the attachment of two biomolecule 'arms' to the alpha telechelic end point of a polymer and fixating the conjugate to the gold surface of SAW and SPR sensor chips with the polymer's other omega chain end. This specific design of a conjugate will be implemented by using a strategy to yield novel double alpha as well as omega telechelic functionalized POx and the success of all cascade reaction steps leading to the final conjugation product will be proven through affinity measurements between covalently bound mannose and ConA. All reactions were performed on a low molecular model level first and then transferred to telechelic and also side chain functionalized polymer systems.},
  subject      = {Polyoxazoline},
  language  = {en}
}
@phdthesis{Uthe2018,
  author    = {Uthe, Friedrich Wilhelm},
  title     = {Identifikation synthetisch-letaler Interaktionen mit dem Tumorsuppressor APC und Beeinflussung von MYC-Proteinmengen durch Translationsinhibition im kolorektalen Karzinom},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166451},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {Der Tumorsupressor APC ist in der Mehrzahl aller F{\"a}lle kolorektaler Karzinome bereits in der initialen Phase der Karzinogenese mutiert. Diese Mutationen f{\"u}hren zu einer aberranten Aktivierung des Wnt-Signalweges sowie zu weiteren die Karzinogenese vorrantreibenden Aktivit{\"a}ten, beispielsweise einem ver{\"a}nderten Migrationsverhalten. Dieser Dissertation zu Grunde liegt die Idee, dass durch die Trunkierung des APC-Proteins aber auch Abh{\"a}ngigkeiten von Genaktivit{\"a}ten entstehen, die zuvor entbehrlich waren. Solche synthetisch letalen Gene sollten in einem high-content shRNA-Screen gefunden werden. F{\"u}r die Durchf{\"u}hrung des Screens wurde ein von der SW480 Kolonkarzinomzelllinie abgeleitetes, isogenes Zellsystem generiert, welches durch Induktion mit Doxyzyklin das vollst{\"a}ndige APC-Allel (FL-APC) exprimiert. Infolge dieser Expression zeigen die Zellen einen weniger malignen Ph{\"a}notyp. Dies spiegelt sich darin wider, dass die Zellen durch FL-APC Expression in ihrer Wnt-Signalwegsaktivit{\"a}t eingeschr{\"a}nkt werden. Doxyzyklininduzierte Zellen sind schlechter in der Lage ohne Adh{\"a}sion zu proliferieren als nicht induzierte Zellen. Andererseits ist ihre F{\"a}higkeit einem FKS-gradienten entlang zu migrieren verbessert. Der shRNA-Screen wurde mit der Decipher shRNA-Bibliothek durchgef{\"u}hrt. Diese enth{\"a}lt 27.500 verschiedene shRNAs mit Interferenzaktivit{\"a}t gegen 5.000 mRNAs, die potentiell pharmakologisch inhibierbare Proteine kodieren. Die besten zwei Kandidaten f{\"u}r eine synthetisch letale Interaktion mit trunkiertem APC, BCL2L1 und EIF2B5 wurden im Verlauf einer Masterarbeit bzw. direkt in dieser Disseration validiert. EIF2B5 zeigte in vitro nach Depletion durch unterschiedliche shRNAs einen di erentiellen Proliferationse ekt bei FL-APC induzierten im Vergleich zu kontrollbehandelten Zellen. Dieser di erentielle E ekt konnte in einem weiteren Modellsystem, SW480 Zellen mit konstitutiver FL-APC Expression, ebenfalls validiert werden. Durch Expression einer shRNA mit Aktivit{\"a}t gegen EIF2B5 werden in beiden Zellsystem die unfolded protein response (UPR) Gene DDIT3 und splXBP1 aktiviert. Interessanterweise werden durch die Expression von FL-APC diese Gene reprimiert. Im Promotor der EIF2B5-mRNA be ndet sich eine Bindestelle f{\"u}r MYC. Es ist denkbar, dass durch die Expression von FL-APC eine globale Ver{\"a}nderung der Genexpression vorgenommen wird, die einerseits eine Repression von EIF2B5 nach sich zieht aber andererseits eine hierdurch ausgel{\"o}ste ER-Stress Antwort verhindert. Eine Inhibition von EIF2B5 ohne diese Adaption andererseits f{\"u}hrt nach diesem Model zu einer UPR-aktivierten Apoptose. In einem zweiten Projekt wurde das {\"u}berraschende Verhalten von Kolonkarzinomzellen untersucht, die nach Zugabe von BEZ235, einem dualen PI3K/mTOR Inhibitor, trotz gegenteiliger Erwartungen MYC-Proteinmengen erh{\"o}hen. Eine Repression wurde erwar- tet, weil die Inhibition von PI3K einerseits zu einer proteasomalen Destabiliserung und andererseits die mTOR Inhibition zu einer verringerten Synthese von MYC f{\"u}hren sollte. W{\"a}hrend bereits gezeigt werden konnte, dass durch einen FOXO-vermittelten Mechanismus MAPK-abh{\"a}ngig die MYC-Expression verst{\"a}rkt wird, wurde in dieser Dissertation die erwartete Translationsinhibition untersucht. BEZ235 inhibiert zwar CAP-abh{\"a}ngige Translation, das MYC Protein wird jedoch aufgrund einer IRES-vermittelten Translation weiterhin exprimiert. Silvestrol, ein Inhibitor der Helikase eIF4A andererseits interveniert mit CAP- und IRES-abh{\"a}ngiger Translation und kann die MYC-Proteinkonzentrationen verringern. Wir konnten zudem feststellen, dass die Applikation von Silvestrol auch in vivo m{\"o}glich und wirksam ist und zudem tolleriert wird. Dies gibt Anlass zur Ho nung, dass eine Intervention der Translation auch im Menschen eine valide Strategie zur Behandlung MYC-getriebener Tumore sein k{\"o}nnte.},
  subject      = {Colonkrebs},
  language  = {de}
}
@article{BossertdeBruinGoetzetal.2016,
  author    = {Bossert, Nelli and de Bruin, Donny and G{\"o}tz, Maria and Bouwmeester, Dirk and Heinrich, Doris},
  title     = {Fluorescence-tunable Ag-DNA biosensor with tailored cytotoxicity for live-cell applications},
  series = {Scientific Reports},
  volume    = {6},
  journal   = {Scientific Reports},
  number    = {37897},
  doi       = {10.1038/srep37897},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-167482},
  year      = {2016},
  abstract  = {DNA-stabilized silver clusters (Ag-DNA) show excellent promise as a multi-functional nanoagent for molecular investigations in living cells. The unique properties of these fluorescent nanomaterials allow for intracellular optical sensors with tunable cytotoxicity based on simple modifications of the DNA sequences. Three Ag-DNA nanoagent designs are investigated, exhibiting optical responses to the intracellular environments and sensing-capability of ions, functional inside living cells. Their sequence-dependent fluorescence responses inside living cells include (1) a strong splitting of the fluorescence peak for a DNA hairpin construct, (2) an excitation and emission shift of up to 120 nm for a single-stranded DNA construct, and (3) a sequence robust in fluorescence properties. Additionally, the cytotoxicity of these Ag-DNA constructs is tunable, ranging from highly cytotoxic to biocompatible Ag-DNA, independent of their optical sensing capability. Thus, Ag-DNA represents a versatile live-cell nanoagent addressable towards anti-cancer, patient-specific and anti-bacterial applications.},
  language  = {en}
}
@phdthesis{HorvatCsotigebHorvat2021,
  author    = {Horvat-Cs{\´o}ti [geb. Horvat], Sonja},
  title     = {Development of Nanocarriers for Treatment and Diagnostics of Aspergillosis},
  doi       = {10.25972/OPUS-23821},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-238218},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {This thesis aimed to evaluate the possibility to use nanoparticles as antifungal drug carriers as well as their potential application in screening and diagnostics of invasive aspergillosis. The interaction of nanogels, superparamagnetic iron oxide nanoparticles (SPIOs) and gold nanoparticles (GNP) with fungal-specific polysaccharides, cells and biofilms was investigated. Firstly, it was evaluated how the charge of nanogels influence their interaction with fungal cells. Linear poly(glycidol)s (pG) and poly(2-methyl-2-oxazoline) (pMOx) polymers were synthesized and further functionalized with thiol groups for preparation of redox responsive nanogels. Results showed that negatively charged nanogels were internalized by the fungi to a much greater extent than positively charged ones. Furthermore, it was investigated how amphiphilicity of polymers used for preparation of nanogels influences nanogel-fungi interaction. It was concluded that nanogels prepared from polymers with degree of functionalization of 10\% had the strongest interaction, regardless the length of the alkyl chain. Moreover, amphotericin B-loaded nanogels had a higher antifungal effect and lower toxicity towards mammalian cells than the free drug. In addition, inverse nanoprecipitation of thiol functionalized pGs was shown to be successful for preparation of nanogels with narrow size distribution. It was also demonstrated that crosslinking of the polymeric coating in hydrogel-like network with thiol functionalized pGs improved the SPIOs imaging performance. Finally, it was investigated whether GNPs could be used as model particles for the assessment of targeting to fungi. Fc dectin-1 was conjugated covalently to GNPs decorated with pGs, and binding affinity towards β-glucans was tested by surface plasmon resonance. In summary, this thesis demonstrated evidence for the potential of pG nanogels and pG coated nanoparticles for antifungal therapy and diagnostics of fungal infections caused by A. fumigatus.},
  subject      = {Therapeutisches System},
  language  = {en}
}
@article{LehmannBaumannLambovetal.2021,
  author    = {Lehmann, Matthias and Baumann, Maximilian and Lambov, Martin and Eremin, Alexey},
  title     = {Parallel polar dimers in the columnar self-assembly of umbrella-shaped subphthalocyanine mesogens},
  series = {Advanced Functional Materials},
  volume    = {31},
  journal   = {Advanced Functional Materials},
  number    = {38},
  doi       = {10.1002/adfm.202104217},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-256343},
  year      = {2021},
  abstract  = {The self-assembly of umbrella-shaped mesogens is explored with subphthalocyanine cores and oligo(thienyl) arms with different lengths in the light of their application as light-harvesting and photoconducting materials. While the shortest arm derivatives self-assemble in a conventional columnar phase with a single mesogen as a repeating unit, the more extended derivatives generate dimers that pile up into liquid crystalline columns. In contrast to the antiparallel arrangement known from single crystals, the present mesogens align as parallel dimers in polar columnar phases as confirmed by X-ray scattering, experimental densities, dielectric spectroscopy, second harmonic generation, alignment, and conductivity studies. UV-vis and fluorescence spectroscopies reveal a broad absorption in the visible range and only weak emission of the Q-band. Thus, these light-collecting molecules forming strongly polar columnar mesophases are attractive for application in the area of photoconductive materials.},
  language  = {en}
}
@phdthesis{Ramirez2024,
  author    = {Ramirez, Yesid A.},
  title     = {Structural basis of ubiquitin recognition and rational design of novel covalent inhibitors targeting Cdu1 from \(Chlamydia\) \(Trachomatis\)},
  doi       = {10.25972/OPUS-19168},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-191683},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2024},
  abstract  = {The WHO-designated neglected-disease pathogen Chlamydia trachomatis (CT) is a gram-negative bacterium responsible for the most frequently diagnosed sexually transmitted infection worldwide. CT infections can lead to infertility, blindness and reactive arthritis, among others. CT acts as an infectious agent by its ability to evade the immune response of its host, which includes the impairment of the NF-κB mediated inflammatory response and the Mcl1 pro-apoptotic pathway through its deubiquitylating, deneddylating and transacetylating enzyme ChlaDUB1 (Cdu1). Expression of Cdu1 is also connected to host cell Golgi apparatus fragmentation, a key process in CT infections. Cdu1 may this be an attractive drug target for the treatment of CT infections. However, a lead molecule for the development of novel potent inhibitors has been unknown so far. Sequence alignments and phylogenetic searches allocate Cdu1 in the CE clan of cysteine proteases. The adenovirus protease (adenain) also belongs to this clan and shares a high degree of structural similarity with Cdu1. Taking advantage of topological similarities between the active sites of Cdu1 and adenain, a target-hopping approach on a focused set of adenain inhibitors, developed at Novartis, has been pursued. The thereby identified cyano-pyrimidines represent the first active-site directed covalent reversible inhibitors for Cdu1. High-resolution crystal structures of Cdu1 in complex with the covalently bound cyano-pyrimidines as well as with its substrate ubiquitin have been elucidated. The structural data of this thesis, combined with enzymatic assays and covalent docking studies, provide valuable insights into Cdu1s activity, substrate recognition, active site pocket flexibility and potential hotspots for ligand interaction. Structure-informed drug design permitted the optimization of this cyano-pyrimidine based scaffold towards HJR108, the first molecule of its kind specifically designed to disrupt the function of Cdu1. The structures of potentially more potent and selective Cdu1 inhibitors are herein proposed. This thesis provides important insights towards our understanding of the structural basis of ubiquitin recognition by Cdu1, and the basis to design highly specific Cdu1 covalent inhibitors.},
  subject      = {Ubiquitin},
  language  = {en}
}
@phdthesis{Drakopoulos2024,
  author    = {Drakopoulos, Antonios},
  title     = {Opioid receptor oligomerization study through fluorescent selective ligands},
  doi       = {10.25972/OPUS-20717},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-207179},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2024},
  abstract  = {Opioid receptors (ORs) are among the most intensively studied members of the G protein-coupled receptor (GPCR) family due to their important role in pain management and their involvement in psychological and neurological disorders. However, currently available opioid drugs exhibit both serious drawbacks, such as addiction, and life-threatening side effects, such as respiratory depression. Contrary to the classic monomeric model, indirect evidence suggests that ORs might form dimers, which could be endowed with a distinct pharmacological profile, and, thus, be exploited to develop innovative drugs. However, direct evidence for the spontaneous formation of OR dimers in living cells under physiological condition are missing. The focus of this thesis was the design, synthesis and characterization of new, highly subtype-selective OR fluorescent ligands to be used as tools for state-of-the-art microscopy methods, such as single molecule microscopy (SMM), in heterologous cells and potentially in native tissue, in order to investigate OR organization and mobility on the surface of intact, living cells, at low/physiological expression levels. The μOR is the OR subtype which plays the most critical role in pain modulation, while mediating the effects of the most powerful analgesic drugs. Also, it is the OR subtype which is mostly responsible for the major adverse effects of the currently marketed opioid drugs. We aimed to develop a new μOR-selective fluorescent ligand with a potential irreversible binding mode. Although the approach was in principle successful, i.e. the labelled cells were visible and distinguishable; this initial attempt was not suitable for SMM due to the ligands' poor selectivity and affinity as well as due to its high background noise. A second generation of the fluorescent ligand was designed; however the synthesis and characterization are part of another doctoral thesis. Lately, δOR has received attention as a promising drug target, due to its distinct pharmacological profile which features low abuse liability and lack of physical dependence. In addition, δOR expression has been associated with cancer regulation in the periphery, thus further highlighting the interest of imaging tools for this receptor. In this thesis, the development and characterization of two new δOR-selective fluorescent probes with excellent optical properties, based on the well-studied ligand naltrindole (NTI) is presented. Their application in SMM studies is currently underway at the group of Prof. Dr. Davide Calebiro at the University of Birmingham. The κOR is a subtype which has also emerged as a drug target due to its low abuse potential. Despite a growing interest in this receptor, κOR-selective fluorescent probes have been particularly scarce in literature. Herein, the design, synthesis and characterization of the first reported set of fluorescent κOR-selective probes with antagonistic properties, based on the established ligand 5'-guanidinonaltrindole (5'-GNTI) is presented. Two of these were employed for SMM experiments to investigate κOR homodimerization, localization and trafficking. Our findings do not support homodimerization of the κOR-bound probe complexes, while showing that the majority of them follow a normal Brownian diffusion on the cell surface.},
  subject      = {Opioidrezeptor},
  language  = {en}
}
@phdthesis{Kappenberger2024,
  author    = {Kappenberger, Jeannette Sarah},
  title     = {Biochemical characterization of the TFIIH translocase XPB from \(Chaetomium\) \(thermophilum\)},
  doi       = {10.25972/OPUS-24409},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-244096},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2024},
  abstract  = {DNA repair and gene expression are two major cellular processes that are fundamental for the maintenance of biological life. Both processes require the enzymatic activity of the super family 2 helicase XBP, which is an integral subunit of the general transcription factor TFIIH. During transcription initiation, XPB catalyzes the initial melting of promoter DNA enabling RNA polymerase II to engage with the coding DNA strand and start gene transcription. In nucleotide excision repair, XPB acts in concert with the other TFIIH helicase XPD causing strand separation around a lesion site. Mutations within the genes encoding XPB or other TFIIH subunits are associated with different cancer types as well as with the autosomal recessive disorders Xeroderma Pigmentosum and trichothiodystrophy and rarely combined features of Xeroderma Pigmentosum and Cockayne syndrome. In the last few years, great progress has been made towards unraveling the structure of TFIIH and its individual subunits including XPB. These structural insights tremendously improved our understandings with respect to the molecular interactions within this intriguing protein complex. However, the underlying regulation mechanisms that functionally control XPB during transcription and repair remained largely elusive. We thus executed the biochemical characterization of this protein to investigate the functional network that regulates XPB within the scaffold of TFIIH. Due to their enhanced stability compared to the human proteins, we utilized the proteins that originate from the thermophilic fungus Chaetomium thermophilum for this purpose as a model organism for eukaryotic TFIIH. The present work provides novel insights into the enzymatic function and regulation of XPB. We could show that both, DNA and the TFIIH subunit p52 stimulate XPB's ATPase activity and that the p52-mediated activity is further boosted by p8, another subunit within TFIIH. Surprisingly, DNA can activate XPB's ATPase activity to a greater extent than its TFIIH interaction partners p52/p8, but when both, i.e. p52/p8 and DNA are present at the same time, p52 dominates the activation and the enzymatic speed is maintained at the level observed through the sole activation of p52/p8. We thus defined p52 as the master regulator of XPB that simultaneously activates and represses XPB's enzymatic activity. Based on a correlative mutagenesis study of the main interface between p52 and XPB that was set into context with recent structural data, a model for the p52-mediated activation and speed limitation of XPB's ATPase was proposed. The research on XPB's ATPase was expanded with the investigation of the inhibition mechanism of XPB's ATPase via the natural compound Triptolide. Furthermore, we investigated XPB's DNA translocase function and could observe that XPB can only perform its translocase movement when it is fully incorporated into core TFIIH and this translocase movement is further enhanced by the nucleotide excision repair factor XPA. Fluorescence polarization measurements with nucleotide analogues revealed that XPB displays the highest affinity towards DNA in the ADP + Pi bound state and its binding is weakened when ADP is bound or the nucleotide is dissociated from the enzyme, suggesting a movement on the DNA during the distinct states of the ATPase cycle. Finally, the well-known and highly conserved RED motif was found to be the crucial element in XPB to enable this translocase movement. Combined, the data presented in this work provide novel insights into the intricate regulation network that controls XPB's enzymatic activity within TFIIH and furthermore show that XPB's enzymatic activity is tightly controlled by various factors.},
  subject      = {DNS-Reparatur},
  language  = {en}
}